[PRE REVIEW]: SBMLToolkit.jl: A Julia package for generating ModelingToolkit models from SBML

[editorialbot]

Submitting author: !--author-handle-->@paulflang<!--end-author-handle-- (Paul F Lang) Repository: https://github.com/SciML/SBMLToolkit.jl Branch with paper.md (empty if default branch): Version: v0.1.21 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

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Thanks for submitting your paper to JOSS @paulflang. Currently, there isn't a JOSS editor assigned to your paper.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (810.6 files/s, 52650.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           16            131             42            955
XML                             10              0              2            888
YAML                             9             12             16            240
Markdown                         4             70              0            212
TeX                              1             12              0            172
TOML                             3              5              0             36
-------------------------------------------------------------------------------
SUM:                            43            230             60           2503
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 389

[editorialbot]

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1101/2022.07.30.502135 is OK
- 10.5334/jors.151 is OK
- 10.1145/3511528.3511535 is OK
- 10.1093/bioinformatics/btg015 is OK
- 10.1093/bioinformatics/btn051 is OK
- 10.1177/0037549703040939 is OK
- 10.1093/bioinformatics/btab782 is OK
- 10.1093/bioinformatics/btw469 is OK
- 10.1093/bioinformatics/bth378 is OK

MISSING DOIs

- 10.21203/rs.3.rs-55125/v1 may be a valid DOI for title: Universal Differential Equations for Scientific Machine Learning

INVALID DOIs

- None

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[paulflang]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[paulflang]

I think the following researchers from the JOSS reviewer list would be suitable candidates to review our work:

• mhucka
• ajbaird
• metelkin

[Kevin-Mattheus-Moerman]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[Kevin-Mattheus-Moerman]

@paulflang thanks for this submission. I am the AEiC on this track and here to help process the first steps. I have just triggered a scope review by the editorial board. This is because of I feel I need some help to determine whether this work is in scope for JOSS. In particular it seems this work is rather small and perhaps narrow in terms of functionality. This scope review should hopefully be completed within two weeks.

[paulflang]

Thanks a lot for taking this up, @Kevin-Mattheus-Moerman . In case it helps for the scope review, let me point you to

• the BioModels database, which highlights the central role of SBML as community standard for systems biology,
• the SBML specification, which shows all the features of the SBML language (note that even core SBML allows so much flexibility in model descriptions, that I am not aware of any software package for any language with full core SBML support -> unfortunately, the SBML Test Suite Database has been down for a while to confirm this),
• and a list of importers for other programming languages, incl. publications.

Unfortunately, I don't have user statistics for the uptake of the Julia programming language in the systems biology community, to help you assess the scale and importance of SBMLToolkit.jl, but judging from recent conferences I've been to, there is a lot of momentum.

[Kevin-Mattheus-Moerman]

@paulflang the editorial board has concluded the scope review for this submission and determined this work is currently not in scope for JOSS. Although the code appears well-packaged, and documented, and includes implemented tests, the core functionality appears to be file import/conversion. As it stands this makes it close to a utility package, which although useful is not in scope for JOSS.

We will now proceed to reject this submission. Note that this rejection does not mean the work is off a poor quality or not useful. Instead it merely means it is not in scope in its current form. We do hope you consider JOSS for any future submissions that have a more extensive functionality (and we also welcome re-submissions).

[Kevin-Mattheus-Moerman]

@editorialbot reject

[editorialbot]

Paper rejected.